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- PDB-9jfb: Crystal structure of L-threonine-O-3-phosphate decarboxylase CobC -

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Basic information

Entry
Database: PDB / ID: 9jfb
TitleCrystal structure of L-threonine-O-3-phosphate decarboxylase CobC
Componentsthreonine-phosphate decarboxylase
KeywordsLYASE / cobalamin / L-threonine-O-3-phosphate decarboxylase / PLP / aminopropanol phosphate
Function / homology
Function and homology information


threonine-phosphate decarboxylase / threonine-phosphate decarboxylase activity / cobalamin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
L-threonine-O-3-phosphate decarboxylase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
threonine-phosphate decarboxylase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJiang, M. / Guo, S. / Chen, X. / Wei, Q. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2108085MC75 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structure of l-threonine-O-3-phosphate decarboxylase CobC from Sinorhizobium meliloti involved in vitamin B 12 biosynthesis.
Authors: Jiang, M. / Guo, S. / Chen, X. / Wei, Q. / Wang, M.
History
DepositionSep 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: threonine-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,42818
Polymers36,1221
Non-polymers1,30617
Water6,503361
1
A: threonine-phosphate decarboxylase
hetero molecules

A: threonine-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,85636
Polymers72,2442
Non-polymers2,61134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area9900 Å2
ΔGint-318 kcal/mol
Surface area25820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.418, 159.418, 159.418
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-417-

NA

21A-851-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein threonine-phosphate decarboxylase / L-threonine-O-3-phosphate decarboxylase


Mass: 36122.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (bacteria) / Gene: cobC / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(ED3)
References: UniProt: A0A499W357, threonine-phosphate decarboxylase

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Non-polymers , 5 types, 378 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.67 Å3/Da / Density % sol: 73.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.1M Bis-Tris pH 7.2, 1.2 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 34268 / % possible obs: 100 % / Redundancy: 10.9 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.056 / Rrim(I) all: 0.184 / Χ2: 0.982 / Net I/σ(I): 5.3 / Num. measured all: 374964
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.2810.71.19634090.7510.9260.3811.2560.883100
2.28-2.37110.90233630.830.9520.2850.9460.91100
2.37-2.4811.30.67834240.8860.9690.2110.710.936100
2.48-2.6111.40.48533820.9350.9830.150.5080.931100
2.61-2.77110.36334190.9610.990.1150.3810.967100
2.77-2.9911.10.26334090.9770.9940.0830.2760.997100
2.99-3.2911.40.18434120.9890.9970.0570.1931.037100
3.29-3.7610.80.13734470.9920.9980.0440.1441.082100
3.76-4.7410.70.1134500.9940.9990.0350.1161.041100
4.74-5010.10.09735530.9930.9980.0320.1021.03699.9

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→39.85 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1846 1621 4.81 %
Rwork0.1545 --
obs0.1559 33713 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→39.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2481 0 68 361 2910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.847
X-RAY DIFFRACTIONf_dihedral_angle_d12.003948
X-RAY DIFFRACTIONf_chiral_restr0.052399
X-RAY DIFFRACTIONf_plane_restr0.009472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.29351360.22862592X-RAY DIFFRACTION97
2.26-2.340.23651410.21492606X-RAY DIFFRACTION97
2.34-2.420.25591220.20612649X-RAY DIFFRACTION97
2.42-2.520.21071270.18412654X-RAY DIFFRACTION98
2.52-2.630.19111440.17382592X-RAY DIFFRACTION97
2.63-2.770.20131310.17052668X-RAY DIFFRACTION98
2.77-2.940.19941420.16152671X-RAY DIFFRACTION99
2.95-3.170.20541420.17092686X-RAY DIFFRACTION99
3.17-3.490.20871440.14692685X-RAY DIFFRACTION100
3.49-40.15881310.1312739X-RAY DIFFRACTION100
4-5.030.1471400.1212736X-RAY DIFFRACTION100
5.04-39.850.15591210.14972814X-RAY DIFFRACTION99

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